def __init__(
self,
name="base",
anchor="base",
target=None,
href=None,
info=None,
comment=None,
extra=None,
autoformat=True,
autoformat_type="markdown",
):
# Custom options from user config that can overwrite base module values
mod_cust_config = getattr(self, "mod_cust_config", {})
self.name = mod_cust_config.get("name", name)
self.anchor = mod_cust_config.get("anchor", anchor)
target = mod_cust_config.get("target", target)
self.href = mod_cust_config.get("href", href)
self.info = mod_cust_config.get("info", info)
self.comment = mod_cust_config.get("comment", comment)
self.extra = mod_cust_config.get("extra", extra)
# Specific module level config to overwrite (e.g. config.bcftools, config.fastqc)
config.update({anchor: mod_cust_config.get("custom_config", {})})
# Sanitise anchor ID and check for duplicates
self.anchor = report.save_htmlid(self.anchor)
# See if we have a user comment in the config
if self.anchor in config.section_comments:
self.comment = config.section_comments[self.anchor]
if self.info is None:
self.info = ""
if self.extra is None:
self.extra = ""
if target is None:
target = self.name
if self.href is not None:
self.mname = '<a href="{}" target="_blank">{}</a>'.format(
self.href, target)
else:
self.mname = target
if self.href or self.info or self.extra:
self.intro = "<p>{} {}</p>{}".format(self.mname, self.info,
self.extra)
# Format the markdown strings
if autoformat:
if self.comment is not None:
self.comment = textwrap.dedent(self.comment)
if autoformat_type == "markdown":
self.comment = markdown.markdown(self.comment)
self.sections = list()
def __init__(self,
name='base',
anchor='base',
target=None,
href=None,
info=None,
comment=None,
extra=None,
autoformat=True,
autoformat_type='markdown'):
# Custom options from user config that can overwrite base module values
mod_cust_config = getattr(self, 'mod_cust_config', {})
self.name = mod_cust_config.get('name', name)
self.anchor = mod_cust_config.get('anchor', anchor)
target = mod_cust_config.get('target', target)
href = mod_cust_config.get('href', href)
info = mod_cust_config.get('info', info)
self.comment = mod_cust_config.get('comment', comment)
extra = mod_cust_config.get('extra', extra)
# Specific module level config to overwrite (e.g. config.bcftools, config.fastqc)
config.update({anchor: mod_cust_config.get('custom_config', {})})
# Sanitise anchor ID and check for duplicates
self.anchor = report.save_htmlid(self.anchor)
# See if we have a user comment in the config
if self.anchor in config.section_comments:
self.comment = config.section_comments[self.anchor]
if info is None:
info = ''
if extra is None:
extra = ''
if target is None:
target = self.name
if href is not None:
mname = '<a href="{}" target="_blank">{}</a>'.format(href, target)
else:
mname = target
if href or info or extra:
self.intro = '<p>{} {}</p>{}'.format(mname, info, extra)
# Format the markdown strings
if autoformat:
if self.comment is not None:
self.comment = textwrap.dedent(self.comment)
if autoformat_type == 'markdown':
self.comment = markdown.markdown(self.comment)
self.sections = list()
def __init__(self, name='base', anchor='base', target=None, href=None, info=None, comment=None, extra=None,
autoformat=True, autoformat_type='markdown'):
# Custom options from user config that can overwrite base module values
mod_cust_config = getattr(self, 'mod_cust_config', {})
self.name = mod_cust_config.get('name', name)
self.anchor = report.save_htmlid( mod_cust_config.get('anchor', anchor) )
target = mod_cust_config.get('target', target)
href = mod_cust_config.get('href', href)
info = mod_cust_config.get('info', info)
self.comment = mod_cust_config.get('comment', comment)
extra = mod_cust_config.get('extra', extra)
# Specific module level config to overwrite (e.g. config.bcftools, config.fastqc)
config.update({anchor: mod_cust_config.get('custom_config', {})})
# See if we have a user comment in the config
if self.anchor in config.section_comments:
self.comment = config.section_comments[self.anchor]
if info is None:
info = ''
if extra is None:
extra = ''
if target is None:
target = self.name
if href is not None:
mname = '<a href="{}" target="_blank">{}</a>'.format(href, target)
else:
mname = target
self.intro = '<p>{} {}</p>{}'.format( mname, info, extra )
# Format the markdown strings
if autoformat:
if self.comment is not None:
self.comment = textwrap.dedent(self.comment)
if autoformat_type == 'markdown':
self.comment = markdown.markdown(self.comment)
self.sections = list()
def __init__(
self,
name="base",
anchor="base",
target=None,
href=None,
info=None,
comment=None,
extra=None,
autoformat=True,
autoformat_type="markdown",
doi=[],
):
# Custom options from user config that can overwrite base module values
mod_cust_config = getattr(self, "mod_cust_config", {})
self.name = mod_cust_config.get("name", name)
self.anchor = mod_cust_config.get("anchor", anchor)
target = mod_cust_config.get("target", target)
self.href = mod_cust_config.get("href", href)
self.info = mod_cust_config.get("info", info)
self.comment = mod_cust_config.get("comment", comment)
self.extra = mod_cust_config.get("extra", extra)
self.doi = mod_cust_config.get("doi", doi)
# Specific module level config to overwrite (e.g. config.bcftools, config.fastqc)
config.update({anchor: mod_cust_config.get("custom_config", {})})
# Sanitise anchor ID and check for duplicates
self.anchor = report.save_htmlid(self.anchor)
# See if we have a user comment in the config
if self.anchor in config.section_comments:
self.comment = config.section_comments[self.anchor]
if self.info is None:
self.info = ""
# Always finish with a ".", as we may add a DOI after the intro.
if len(self.info) > 0 and self.info[-1] != ".":
self.info += "."
if self.extra is None:
self.extra = ""
self.doi_link = ""
if type(self.doi) is str:
self.doi = [self.doi]
if len(self.doi) > 0:
doi_links = []
for doi in self.doi:
# Build the HTML link for the DOI
doi_links.append(
f' <a class="module-doi" data-doi="{doi}" data-toggle="popover" href="https://doi.org/{doi}" target="_blank">{doi}</a>'
)
self.doi_link = '<em class="text-muted small" style="margin-left: 1rem;">DOI: {}.</em>'.format(
"; ".join(doi_links))
if target is None:
target = self.name
if self.href is not None:
self.mname = '<a href="{}" target="_blank">{}</a>'.format(
self.href, target)
else:
self.mname = target
if self.href or self.info or self.extra or self.doi_link:
self.intro = "<p>{} {}{}</p>{}".format(self.mname, self.info,
self.doi_link, self.extra)
# Format the markdown strings
if autoformat:
if self.comment is not None:
self.comment = textwrap.dedent(self.comment)
if autoformat_type == "markdown":
self.comment = markdown.markdown(self.comment)
self.sections = list()
